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Open Free Energy

@openfree.energy
122 followers 27 following 42 posts
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Open Free Energy @openfree.energy · 04/09/2026
If you use OpenFE, please take this survey to help us improve our documentation and training materials! docs.google.com/forms/d/e/1F...
docs.google.com
OpenFE User Survey 2026
The Open Free Energy project is working to improve our documentation and training materials, to empower users to get started faster and accomplish more with our software. We need your feedback to help...
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Open Free Energy @openfree.energy · 04/08/2026
We’ve launched an OpenFE failure cases repo! Share reproducible crashes, NaNs, and high errors. Contribute here: github.com/OpenFreeEner...
github.com
GitHub - OpenFreeEnergy/openfe-failure-cases: A collection of reproducible openfe protocol failure cases resulting in NaN results.
A collection of reproducible openfe protocol failure cases resulting in NaN results. - OpenFreeEnergy/openfe-failure-cases
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Open Free Energy @openfree.energy · 21/07/2026
The first OpenFE office hours is happening now! Drop in and ask us... just about anything. us06web.zoom.us/j/8786874122...
us06web.zoom.us
Join our Cloud HD Video Meeting
Zoom is the leader in modern enterprise cloud communications.
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Open Free Energy @openfree.energy · 07/07/2026
If you're at #CCPBioSim2026, look for @ialibay.bsky.social and Joshua Horton!
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Michael Shirts @michaelshirts.bsky.social · 22/06/2026
'Alchemical' was not an allowed word in the NYT 'Spelling Bee' today.
Meme of Michael Jordan saying ". . . and I took that personally"
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Open Free Energy @openfree.energy · 21/05/2026
This study has been two years in the making and the results have already been widely discussed and compared against, but the paper is finally out in JCIM today! pubs.acs.org/doi/10.1021/...
pubs.acs.org
Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE
Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav...
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Open Free Energy @openfree.energy · 30/04/2026
openfe now supports simulations of membrane proteins! openfree.energy/science/upda...
openfree.energy
openfe v1.11: Introducing support for membrane systems
We are pleased to announce the release of openfe version 1.11!
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Open Free Energy @openfree.energy · 29/04/2026
There's some deep insight in this blog post and I'll be thinking about it for a while.
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Open Free Energy @openfree.energy · 31/03/2026
See you in Bristol this summer! Our Science Lead @ialibay.bsky.social will be at the CCPBioSim Biomolecular Simulation Conference, July 6-8th, to talk about OpenFE. shop.bris.ac.uk/conferences-...
shop.bris.ac.uk
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Open Free Energy @openfree.energy · 10/03/2026
Modern molecular modeling needs a new mode of software development. Consortia like Open Free Energy build shared tools and release code under open licenses. @omsf.io aligns incentives across stakeholders, enabling an ecosystems that elevates the entire community. pubs.acs.org/doi/10.1021/...
pubs.acs.org
The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling
The increasing importance and predictive power of modern molecular modeling, driven by physics- and machine-learning-based methods, necessitates a new collaborative architecture to replace the isolate...
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Open Force Field @openforcefield.org · 18/02/2026
We’re pleased to announce the 2026 OpenFF Virtual Workshops! Please join us in March and April for workshops on: - Simulating Post-Translationally Modified Proteins with the OpenFF Rosemary Alpha - Fitting a SMIRNOFF Force Field with PyTorch Details linked: docs.openforcefield.org/en/latest/wo...
docs.openforcefield.org
2026 OpenFF Workshops — OpenFF Ecosystem documentation
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Open Free Energy @openfree.energy · 17/02/2026
Check out the recent webinar that our own Alyssa Travitz gave to @sbgrid.bsky.social, introducing our software! youtu.be/nCvg13F9Pco
youtu.be
Open Free Energy
YouTube video by SBGrid Consortium
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SBGrid Consortium @sbgrid.bsky.social · 09/02/2026
Join our software webinar on February 10th to hear from Alyssa Travitz of the @omsf.io on @openfree.energy: An Open Source Ecosystem for Calculating Free Energies. Tuesday, February 10, 2026 - 12:00pm ET Register here: buff.ly/N7AYdjp #SBGrid #Webinars #StructuralBiology
buff.ly
Webinars
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
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Ethan Holz @ethanholz.com · 05/02/2026
Hey folks, @omsf.io is hiring a UX Engineer, our first in the org! We are looking for someone to work with us to build new experiences for computational chemists on a part-time contract basis! If this sounds cool, please apply! We would love to have you! omsf.io/community/jo...
omsf.io
UX Engineer
The Open Molecular Software Foundation (OMSF) builds open-source infrastructure and tooling for computational molecular science. We’re looking for a UX Engineer who can ship polished, usable web exper...
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David L. Dotson @dotsdl.bsky.social · 22/01/2026
What if you could tap into the computational power of thousands of volunteers worldwide to accelerate your drug discovery efforts? That’s what we’ve done by integrating alchemiscale and @openfree.energy with Folding@Home! Read more: alchemiscale.org/advancements... #openscience #drugdiscovery
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David L. Dotson @dotsdl.bsky.social · 14/01/2026
In October of 2025 we released alchemiscale v0.7.0, and followed this up with v0.7.1 and v0.7.2. We wanted to take a moment to highlight these releases, and the improvements they bring for @openfree.energy users! alchemiscale.org/advancements... #compchem #opensource #alchemistry #openscience
alchemiscale.org
advancements in alchemiscale v0.7
In October of this year we released alchemiscale v0.
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John Chodera @jchodera.bsky.social · 12/01/2026
OpenBind is a new open science effort to dramatically increase the number of protein:ligand structures in the PDB, pairing this with high-quality affinity data to enable a new generation of predictive structure and affinity models for drug discovery. Check it out: openbind.ai
openbind.ai
Home | openbind.uk
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Free Energy Workshop 2025 @feworkshop.bsky.social · 05/01/2026
Exciting news! We have a new website: omsf.io/alchemistry Your one-stop shop for everything related to our conference community. 🎉 BTW, registration is now open, so head over to secure your spot! We'll be sharing updates and details about the event. Bookmark it as there's plenty more to come!
omsf.io
Alchemistry Workshop in Free Energy Methods for Drug Design - Alchemistry
Annual conference on Free Energy Methods in Drug Discovery
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Open Free Energy @openfree.energy · 18/12/2025
To our knowledge, this is the first study to report binding free energy benchmarks on a cross-company collection of proprietary datasets. We couldn't have done it without the hard work of our amazing partner companies!
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Open Free Energy @openfree.energy · 18/12/2025
Across a total of 1,700 ligands, OpenFE shows robust performance, generates reproducible results, and achieves both sufficient throughput and rapid convergence. Our protocol: - ranks compounds about as well as commercial solutions - does not require fine-tuning settings for each system
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Open Free Energy @openfree.energy · 18/12/2025
OpenFE is ready for production! chemrxiv.org/engage/chemr... In collaboration with our industry partners, we ran benchmarking simulations of our hybrid-topology RBFE protocol on a large collection of both public and private protein-ligand binding datasets. #compchem
chemrxiv.org
Large-scale collaborative assessment of binding free energy calculations for drug discovery using OpenFE
Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav...
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Open Force Field @openforcefield.org · 17/11/2025
Jeff Wagner and Jen Clark ran a workshop at the @mdanalysis.bsky.social UGM in Arizona last week, in coordination with the @openfree.energy team.
Left to right: Mike Henry, Alyssa Travitz, Irfan Alibay, Jennifer Clark, Jeffrey Wagner, Hugo McDermott-Opeskin
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Open Free Energy @openfree.energy · 11/11/2025
Our docs have you covered! We have a "cookbook" demonstrating how to use our API for a variety of tasks in setting up free energy calculations. docs.openfree.energy/en/latest/co...
docs.openfree.energy
Cookbook — OpenFE documentation
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Open Free Energy @openfree.energy · 11/11/2025
Our command line interface (CLI) is designed to provide easy access to our tested, production-ready workflow. But if you are developing new methods or pioneering workflows, you may need the power and flexibility of our application programming interface (API) in #Python. #compchem
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Open Free Energy @openfree.energy · 24/10/2025
We've just released openfe v1.7, which includes includes new protocols for Separated Topologies and Absolute Binding Free Energies, as well as up to 2x faster simulations using the default settings. openfree.energy/science/upda...
openfree.energy
openfe v1.7.0: SepTop, ABFEs, faster simulations, and more!
We are pleased to announce the release of openfe version 1.7.0!
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Open Free Energy @openfree.energy · 14/10/2025
We tested Sage 2.3.0rc2 from @openforcefield.org in RBFE benchmarks and found it improves accuracy on some of our benchmark systems like p38. Can't wait to see the GNN charge model become default!
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Open Force Field @openforcefield.org · 10/10/2025
We’re pleased to announce Sage 2.3.0 Release Candidate 2 (rc2)! Sage 2.3.0 will be the first OpenFF force field to use the AshGC neural network charge model, which was trained to AM1BCC ELF10 charges, and allows for rapid charge assignment for molecules with hundreds or thousands of heavy atoms.
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Free Energy Workshop 2025 @feworkshop.bsky.social · 23/09/2025
Save the date, my fellow computational alchemists! The upcoming '26 Workshop on Free Energy Methods in Drug Design will be held in Barcelona, Spain, on May 4-6, 2026. The registration link will be sent soon!
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Open Free Energy @openfree.energy · 11/09/2025
OpenFE is being used to predict affinity of molecular glues! Check out the new preprint from the team at Ternary Therapeutics: chemrxiv.org/engage/chemr...
chemrxiv.org
Optimizing Molecular Glues Using Free Energy Perturbation and Cofolding Methods
Molecular glues, a class of small molecules that induce protein-protein interactions, hold significant promise as a therapeutic modality, offering access to new biology unlocking new protein targets w...
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Open Free Energy @openfree.energy · 27/08/2025
You can find more information starting on slide 20 in our February 2025 update presentation: zenodo.org/records/1486...
zenodo.org
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Open Free Energy @openfree.energy · 27/08/2025
To address these challenging cases, the Open Force Field Intitiative provides a tool, “BespokeFit,” for generating custom parameters for the specific chemistry of a target molecule. These custom (or “bespoke”) parameters can be used in RBFE calculations in OpenFE.
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Open Free Energy @openfree.energy · 27/08/2025
Our default force field, OpenFF “Sage,” works well on a wide variety of organic molecules relevant to drug design. However, projects involving more exotic functional groups may be limited by low force field accuracy.
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Open Free Energy @openfree.energy · 27/08/2025
Did you know you can use custom force field parameters in OpenFE? Try out this cookbook to learn more! docs.openfree.energy/en/latest/co... #compchem
docs.openfree.energy
BespokeFit: Using bespoke force field parameters with OpenFE protocols — OpenFE documentation
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Open Free Energy @openfree.energy · 19/08/2025
This is such cool work. Ivan from the Chodera Lab is implementing a protein mutation protocol in OpenFE, and we can't wait to see what incredible studies people do with it!
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Open Free Energy @openfree.energy · 24/06/2025
It's great to see this work in print! It's not on our roadmap this year, but in the longer term we are interested in optimizing replica spacing and will look closely at your method.
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Open Free Energy @openfree.energy · 17/06/2025
But the ability of Boltz-2 to predict affinity opens up new possibilities for drug design workflows, like the Affinity Funneling approach that David Pearlman describes here. medium.com/@dapscience/...
medium.com
Boltz-2 vs. FEP? The Wrong Question. Here’s Why They’re Stronger Together
The Boltz-2 AI model lays claim to some amazing improvements in ligand affinity prediction. The greatest value may be in the realms of…
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Open Free Energy @openfree.energy · 17/06/2025
Alchemical free energy simulations will remain a crucial step in teh drug design process for their accuracy and reliability, especially in binding pockets that rearrange to accommodate different ligands. www.deepmirror.ai/post/boltz-2... #opensource #compchem #boltz2
deepmirror.ai
Evaluating Boltz-2 on Real Drug Targets: Does it work? | deepmirror
Evaluating Boltz-2 on Real Drug Targets: Does it work?
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Open Free Energy @openfree.energy · 13/06/2025
It's exciting to see our software used as a benchmark for cutting-edge AI methods!
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David L. Dotson @dotsdl.bsky.social · 28/05/2025
This poster illustrates the substantial flexibility of the open source @openfree.energy ecosystem, enabling unconventional approaches for applying free energy methods. As this ecosystem continues to evolve, I'm excited to see what users do with the advancements we make!
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Open Free Energy @openfree.energy · 15/05/2025
If you weren't at @feworkshop.bsky.social in Boston last week, you missed Hannah Baumann giving the first sneak peek at results from our partner benchmarking study! Fortunately for you, Josh Horton wrote up a blog post about the early results: blog.omsf.io/the-free-ene... #compChem
blog.omsf.io
The Free Energy of Everything: Benchmarking OpenFE
Written by: Josh Horton, PhD Who is OpenFE and what do they do? Open Free Energy (OpenFE) sits at the nexus of academia and industry. We are developing an open-source software ecosystem for alchem...
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Karmen Condic-Jurkic @karmencj.bsky.social · 09/05/2025
Aniket Margakar from Boehringer demonstrated how they use @omsf.io tools in house, praising both the tools and teams -- that's what we like to hear! He highly recommends NAGL and bespokefit for fast charge assignment and parameterization, and @openfree.energy for FE calcs
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Karmen Condic-Jurkic @karmencj.bsky.social · 09/05/2025
@jenkescheen.bsky.social showcased his work on @asapdiscovery.bsky.social and more recently with CharmTx, combining ML and more traditional free energy calculations. A lot, if not all, of his work is based on @openfree.energy, #openforcefield, and #alchemsicale. Read his papers for more details!
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Open Free Energy @openfree.energy · 30/04/2025
The Ecosystem Infrastructure team at @omsf.io (@ethanholz.com and David Swenson) built a tool for running github actions on self-hosted runners. Not the first such tool anyone's ever built, but designed to meet the particular needs of our community, and they delivered! blog.omsf.io/introducing-...
blog.omsf.io
Introducing OMSF Self-Hosted Runners
Written by: Ethan Holz Today marks the official launch of almost a year of work from the OMSF Ecosystem Infrastructure team to deliver a solution for Self-Hosted GitHub Actions runners. This directiv...
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Open Free Energy @openfree.energy · 30/04/2025
Thanks for your great work on this project. We love the result!
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Open Free Energy @openfree.energy · 29/04/2025
We just dropped a new minor release of the openfe software, v1.4.0! It adds several quality-of-life improvements to the command line interface, especially to the `gather` command. openfree.energy/release/2025... #opensource #compchem
A screenshot from the linked page, which reads "An example of how a results table might look as of v1.4.0)" and shows a cleanly-formatted table, including borders.
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OMSF @omsf.io · 22/04/2025
in his blog, our very own Mike Henry demonstrates a powerful, useful skill - CONTAINERIZING. if you are looking for a good how-to on packaging tools, look no further.
blog.omsf.io
Dockerize a Tool
Written by: Mike Henry, PhD Source: https://www.henrymike.com/dockerize-a-tool.html Curious about how to containerize your scientific tools for smoother collaboration and deployment? In this post, Mi...
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Open Free Energy @openfree.energy · 01/04/2025
They report that "The output structures of [AI co-folding model] DragonFold can be readily ported into OpenFE with minimal post-processing." We are glad to hear this feedback, and congratulations on this exciting work!
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Open Free Energy @openfree.energy · 01/04/2025
Their framework was as accurate as approaches that use conventional docking methods, while being much faster.
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Open Free Energy @openfree.energy · 01/04/2025
Researchers at Charm Therapeutics have developed a hybrid framework for small molecule lead optimization in early-stage #DrugDiscovery. It incorporates both an #AI co-folding method and our protocol for calculating relative binding free energies. chemrxiv.org/engage/chemr...
chemrxiv.org
Leveraging Alchemical Free Energy Calculations with Accurate Protein Structure Prediction
Small-molecule lead optimisation in early-stage drug discovery is broadly supported by computational chemistry approaches throughout industry. Over the last decade, Free Energy Perturbation (FEP) has ...
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Open Free Energy @openfree.energy · 26/03/2025
Ready to start using OpenFE? Our documentation includes tutorials on how to use different aspects of our tooling: docs.openfree.energy/en/stable/tu... #opensource #compchem
docs.openfree.energy
Tutorials — OpenFE documentation
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